Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ... Journal of the American Chemical Society 137 (7), 2695-2703, 2015 | 915 | 2015 |

Computations of standard binding free energies with molecular dynamics simulations Y Deng, B Roux The Journal of Physical Chemistry B 113 (8), 2234-2246, 2009 | 562 | 2009 |

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials J Wang, Y Deng, B Roux Biophysical journal 91 (8), 2798-2814, 2006 | 391 | 2006 |

Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant Y Deng, B Roux Journal of Chemical Theory and Computation 2 (5), 1255-1273, 2006 | 316 | 2006 |

Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules Y Deng, B Roux The Journal of Physical Chemistry B 108 (42), 16567-16576, 2004 | 234 | 2004 |

Modeling local structural rearrangements using FEP/REST: application to relative binding affinity predictions of CDK2 inhibitors L Wang, Y Deng, JL Knight, Y Wu, B Kim, W Sherman, JC Shelley, T Lin, ... Journal of chemical theory and computation 9 (2), 1282-1293, 2013 | 180 | 2013 |

Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model D Shivakumar, Y Deng, B Roux Journal of chemical theory and computation 5 (4), 919-930, 2009 | 171 | 2009 |

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations Y Deng, B Roux The Journal of chemical physics 128 (11), 03B611, 2008 | 149 | 2008 |

Accurate modeling of scaffold hopping transformations in drug discovery L Wang, Y Deng, Y Wu, B Kim, DN LeBard, D Wandschneider, M Beachy, ... Journal of chemical theory and computation 13 (1), 42-54, 2017 | 96 | 2017 |

Accurate calculation of relative binding free energies between ligands with different net charges W Chen, Y Deng, E Russell, Y Wu, R Abel, L Wang Journal of chemical theory and computation 14 (12), 6346-6358, 2018 | 75 | 2018 |

Vibrational energy relaxation of polyatomic molecules in liquids: The solvent’s perspective Y Deng, RM Stratt The Journal of chemical physics 117 (4), 1735-1749, 2002 | 57 | 2002 |

High-frequency vibrational energy relaxation in liquids: The foundations of instantaneous-pair theory and some generalizations Y Deng, BM Ladanyi, RM Stratt The Journal of chemical physics 117 (23), 10752-10767, 2002 | 47 | 2002 |

Accurate and reliable prediction of the binding affinities of macrocycles to their protein targets HS Yu, Y Deng, Y Wu, D Sindhikara, AR Rask, T Kimura, R Abel, L Wang Journal of Chemical Theory and Computation 13 (12), 6290-6300, 2017 | 41 | 2017 |

Enhancing water sampling in free energy calculations with grand canonical Monte Carlo GA Ross, E Russell, Y Deng, C Lu, ED Harder, R Abel, L Wang Journal of Chemical Theory and Computation 16 (10), 6061-6076, 2020 | 38 | 2020 |

Methods and systems for calculating free energy differences using an alchemical restraint potential L Wang, Y Deng, Y Wu, KIM Byungchan, RL Abel US Patent 10,726,946, 2020 | 3 | 2020 |

Molecular dynamics calculation of absolute binding free energy: Aromatic ligands bind to a nonpolar cavity of T4 lysozyme. YQ Deng, B Roux ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 228, U254-U254, 2004 | 1 | 2004 |

Computational screening of candidate compounds L Wang, Y Deng, Y Wu, KIM Byungchan, RL Abel US Patent App. 16/929,591, 2021 | | 2021 |

Discovery of potent hits and solving ADME challenges with free energy perturbation and deep learning S Mondal, J Greenwood, S Feng, P Ghanakota, S Rafi, B Kim, Y Deng, ... ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019 | | 2019 |

Enhanced sampling, free energy calculations, and drug discovery L Wang, E Harder, R Abel, Y Wu, Y Deng, J Kaus ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 257, 2019 | | 2019 |

Protein-ligand binding free energy calculations for challenging systems R Abel, L Wang, H Yu, W Chen, E Harder, Y Deng, K Borrelli ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 255, 2018 | | 2018 |